h_mov_new_fname = os.path.join(
os.path.dirname(p_mov),
params.output.prefix + params.output.suffix.join(
os.path.splitext(os.path.basename(p_mov))))
assert os.path.abspath(h_mov_new_fname) != os.path.abspath(
p_mov), 'output filename is same as input filename'
print 'Saving output structure to {}'.format(h_mov_new_fname)
h_mov_new.write_pdb_file(file_name=h_mov_new_fname)
t_end = time.time()
print pretty_string('\n===========================>').bold()
print pretty_string('Finished!').bold()
print pretty_string('Total Runtime: {!s}'.format(
time.strftime("%H hours:%M minutes:%S seconds",
time.gmtime(t_end - t_start)))).bold()
print pretty_string('Avg/Structure: {!s}'.format(
time.strftime("%H hours:%M minutes:%S seconds",
time.gmtime(
(t_end - t_start) / len(params.input.pdb))))).bold()
print pretty_string('===========================>').bold()
#######################################
if __name__ == '__main__':
from giant.jiffies import run_default
run_default(run=run,
master_phil=master_phil,
args=sys.argv[1:],
blank_arg_prepend=blank_arg_prepend)
pruning_rmsd=params.options.pruning_rmsd,
in_place=True,
verbose=params.settings.verbose)
# Update the atoms numbering
final.sort_atoms_in_place()
# Write output file
filename = os.path.splitext(pdb)[0] + params.output.suffix + '.pdb'
log('Writing output structure to {}'.format(filename))
final.write_pdb_file(file_name=filename,
crystal_symmetry=obj.crystal_symmetry())
log.heading('FINISHED')
log.heading('Final Parameters')
log(master_phil.format(params).as_str().strip())
return
############################################################################
if __name__ == '__main__':
from giant.jiffies import run_default
run_default(run=run,
master_phil=master_phil,
args=sys.argv[1:],
blank_arg_prepend=blank_arg_prepend,
program=PROGRAM,
description=DESCRIPTION)
dataset_prefix=params.input.xtal_name,
out_dir=params.output.out_dir,
params=params,
)
logging.info("Plotting occupancy, bfactor and mean |Fobs-Fcalc| "
"for each simulated occupancy")
for simul_occ in np.arange(
params.validate.options.start_simul_occ,
params.validate.options.end_simul_occ,
params.validate.options.step_simulation,
):
# TODO remove duplication of this code: utils.get_minimum_fofc: 59
csv_name = params.exhaustive.output.csv_prefix + "_occ_{}_b_{}.csv".format(
str(simul_occ).replace(".", "_"),
str(params.validate.options.set_b).replace(".", "_"),
)
scatter_plot(csv_name,
title_text="Phenix.fmodel at occ {}".format(simul_occ))
logging.info("Validation script finished")
if __name__ == "__main__":
from giant.jiffies import run_default
run_default(run=run, master_phil=master_phil, args=sys.argv[1:])
